On January 27, 1500 people marched in Timika demanding a referendum on the future status of West Papua, a former Dutch colony that has been occupied by Indonesia since 1962.
The rally took place without being attacked, despite recent violent incidents in the area.
On January 24, nine people, including a US and a South African citizen, were shot and wounded by unidentified attackers at the nearby Freeport gold and copper mine.
On December 16, independence leader Kelly Kwalik was assassinated by police.
Rally coordinator Mario Pigei, of the West Papua National Committee, called for the international community to engage in direct dialogue with West Papuan representatives, the January 28 Jakarta Post said.
Pigei told the rally that dialogue between West Papua and Indonesia through the "special autonomy" process, initiated after the 1998 overthrow of the Suharto dictatorship, was not addressing issues of human rights abuses, land rights, economic marginalisation and poverty.
He called on European countries to stop funding the "special autonomy" process, saying that 60% of the money was spent on military operations. He condemned the killing of Kwalik and called for the withdrawal of the Indonesian army and police.
The Post said Pigei also called for an international investigation into the Freeport shootings.
A January 27 statement by the Jayapura-based West Papua National Authority said rallies calling for a referendum were taking place across West Papua.
WPNA National Congress chairperson, the Reverend Terry Yoku, said: "It's almost half a century, 48 years now, since the Indonesian republic threw its net around us. Look at the failure. Listen to the lies.
"Only extremists and empty heads would invest in the Indonesian model that we know."
The call for a referendum is in opposition to Indonesia's offers of various forms of autonomy that fall short of full self-determination for West Papua,
West Papuans can still be arrested or shot for raising their national flag, the Morning Star.
The call is also a rejection of the 1969 "Act of Free Choice", a process in which the Indonesian army selected a small number of Papuan "representatives" and had them "vote" for incorporation into Indonesia at gunpoint.
The United Nations still recognises the "Act of Free Choice" as the legal basis for West Papua belonging to Indonesia.
Ongoing Western support for the Indonesian occupation is related to West Papua's rich mineral and forestry resources prolonged it.
The Indonesian military directly control economic activity in West Papua, particularly the highly profitable illegal logging industry. Western economic interests, particularly Australian, are mainly in mining.
West Papuans have had land stolen. Ecological destruction has rendering other land unusable. In the cities, Papuans are denied jobs, which are given to Indonesian migrants.
Indicators for health, education and food security are worse for Papuans than other Indonesian citizens.
The Summer 2009/10 edition of Australian Options Magazine said: "A death toll of 100,000 is routinely quoted, although this figure has never been, nor can it be, substantiated.
"Torture, rape, arson and forced relocation have been common and are well documented …
"The Papuans are also suffering a demographic catastrophe: in 1971 they made up 96% of the population, today they are estimated to make up less than 50%, and are a distinct minority in the towns and cities."
The huge US- and- Australian-owned Freeport mine has used the Indonesian occupation to operate without any environmental regulation. It has displaced people both directly and through the poisoning of waterways and land.
The January 21 Post said the Indonesian National Commission on Human Rights had accused Freeport of lacking transparency in the disbursement of the meagre 1% of profits the company is supposed to spend on local development under a 1995 agreement.
The Free Papua Movement (OPM), which resisted the Indonesian occupation since the 1960s, has denied claims by the army that it was responsible for the Freeport shootings.
Several similar attacks took place in 2009, including the July 11 killing of Australian mine technician Drew Grant.
Instead, the OPM suggested elements in the Indonesian military were responsible for the shootings to stymie peace talks.
Peter King, convenor of the West Papua Project at Sydney University agreed. He told Radio Australia on January 26: "Without trouble in West Papua, the military has difficulty trying to justify the large presence it does have — thousands of troops on the ground."
The January 29 Post said shell casings found at the scene were the type "used in M-16, SS-1, Steyr and AK-47 assault rifles, which are issued to the military and police".
The poorly armed OPM lacks access to such weapons.